Module 1.1 Biochemistry Basics SBI4U PDF

SBI4U Module 1 1.1: Biochemistry Basics  Chemistry in Living Systems Elements: simplest form of a substance - cannot be broken down any further without changing what it is. Atom: the actual basic unit of an element - composed of protons, neutrons, and electrons. ...

SBI4U Module 1 1.1: Biochemistry Basics  Chemistry in Living Systems Elements: simplest form of a substance - cannot be broken down any further without changing what it is. Atom: the actual basic unit of an element - composed of protons, neutrons, and electrons.  The Atom Just like cells are the basic unit of life, the atom is the basic unit of matter. They are very small. If placed side by side one million would stretch a distance of 1cm.  The Atom The atom is made up of 3 subatomic particles: – protons, neutrons, and electrons. Electrons are not present in the nucleus of the atom, instead they move around the nucleus of the atom and form an electron cloud. Subatomic Location Charge Particle Proton Nucleus + Neutron Nucleus Neutral Electron Orbitals -  The Atom Example: a helium atom. NEUTRON NUCLEUS PROTON - + + ELECTRON - Atomic Number = 2 (protons) Atomic Mass = 4 (protons + neutrons)  Isotopes Isotopes are atoms of the same element that have a different number of neutrons. Some isotopes are radioactive. This means that their nuclei is unstable and will break down at a constant rate over time. There are several practical uses for radioactive isotopes: 1. Carbon dating 2. Tracers 3. Kill bacteria / cancer cells Periodic Table of the Elements  Elements in Focus We will focus on non-metals such as carbon, hydrogen, oxygen, nitrogen, sulphur and some metals such as sodium, potassium, calcium and magnesium. You must be familiar with the names, symbols, and bonding capacity of these elements. The bonding capacity is the number of bonds that an atom can make. Atom Bonding Capacity H 1 O 2 N 3 S 2 C 4 When two atoms share two electrons between them this produces a single bond. When they share four electrons, it is a double bond. When they share six electrons, it produces a triple bond. Periodic Table of the Elements The group number tends to correspond with the bonding capacity of an atom. Group 1 elements’ atoms tend to make one bond, group 2 elements’ atoms tend to make two bonds, etc. Exception: Group 8 elements tend to be unreactive and do not readily form bonds.  Carbon Bonding Carbon (C) has four electrons in its outermost shell. These electrons are called valence electrons. To make one covalent (this type of bond is based on sharing electrons) bond, C can share an electron with another atom. Lewis dot diagrams (showing only valence electrons) for hydrogen and carbon. Methane, CH4  Bonding Structure Diagrams Electrons in the last energy level can be represented as dots beside the chemical symbol of the element. This is called the electron dot diagram or Lewis Structure. These structures show the shared electrons as well as the other electrons in the last energy level. The shared electrons can also be replaced by lines as shown in the last column. In ethylene, two carbon atoms share four electrons, creating a double bond. In acetylene 2 carbon atoms share 6 electrons, creating a triple bond.  Common Elements The cell is a complex chemical factory containing some of the same elements found in the nonliving environment. The most common elements in living systems are: carbon (C), hydrogen (H), oxygen (O), and nitrogen (N). Most atoms in living systems are found as molecules (2 or more non-metal atoms bonded together). Common Elements  Two Types of Compounds Organic compounds - contain C, H, and O in some typical ratios - usually referred to as chemicals of life – Carbohydrates, Proteins, Lipids, Nucleic Acids Inorganic compounds - usually "support" life - no specific ratio of C, H, and O – e.g. water (H2O), carbon dioxide (CO2)  Interactions Within Molecules Intramolecular forces: chemical bonds within a molecule – Non-polar Covalent Bonds: 2 non-metal atoms share electrons equally – Polar Covalent Bonds: when one atom attracts electrons more than the other, it creates a polar molecule. (A molecule having a slightly positive region and a slightly negative region.)  Interactions Between Molecules Intermolecular forces: forces of attraction between molecules – Hydrogen Bonding: a weak bond between a molecule with a partial negative region containing an oxygen, nitrogen, or fluorine atom and a hydrogen atom in an adjacent molecule with a partial positive charge. – Hydrophobic Interactions: when non-polar molecules group together to stay away from polar molecules.  Organic Chemistry Organic chemistry is sometimes called carbon chemistry since organic molecules form from a carbon frame. Carbon can form four bonds from a single atom and has a unique ability to make long chains with itself. This is called catenation. Carbon molecules can make long chains, as well as chains that branch. When carbon is bonded to hydrogen alone, the type of compound formed is called a hydrocarbon. Hydrocarbons are organic molecules. Ethylene – linear hydrocarbon with a triple bond Ethane – linear hydrocarbon Isobutane – branched hydrocarbon  Functional Groups An atom or group of atoms attached to a molecule that gives the molecule particular chemical and physical properties. The next slide shows a chart of biologically important functional groups. Functional Groups